Oxygen and stable carbon isotope records along the growth direction on shells of the bivalve species Astarte borealis and Serripes groenlandicus reliably record all important aspects of the bottom water hydrography in the shallow southeastern Kara Sea, despite uncertainties about the isotopic range due to sparse sampling and the possibility of growth rate changes. Changing freshwater supply from the rivers Ob and Yenisei is the main cause for seasonal temperature and salinity variations near the three sampling locations in 20 to 70 m water depth as suggested by CTD measurements and modeling. Peak winter salinity of the simulated hydrographic data series and peak winter values in the isotope records follow negative trends, which indicate a freshening of the bottom water due to an increasing fraction of river water during the 1990s. This freshening affected the whole Kara Sea, and coincided with a lowering of regional air pressure gradients, as indicated by the declining Arctic oscillation index. The resulting weakening of the prevailing southwesterly winds diminished the inflow of saline Atlantic-derived water from the Barents Sea through the Kara Strait in the southwest, and, additionally, reduced the export of river water toward the north and northeast into the Arctic basin. Saline Atlantic-derived water thus was replaced by freshwater, which was successively accumulated in the Kara Sea and accordingly imprinted on the stable isotope composition of the bivalve shells. The 1990s freshening in the Kara Sea thus may be caused by natural variations rather than being a signal for global change.